After you clear areas and bosses in the game, you earn Prize Coins. Once you have most of these, you will be able to challenge Mr. Foo. Mr. Foo is a collector and he collected the Pokéballs that fell out of the Phobos Army planes.

The difference in the playing field when against Mr. Foo...there are 7 columns to put Pokémon in instead of the usual 5, this adds more combinations possible with up to a 7 Pokémon long row

The same game dynamics exist here including Trozei Mode allowing for small combinations. Keep at this and you may find some rare Pokémon that are found nowhere else